NM_000546.6(TP53):c.946C>A (p.Pro316Thr) AND Li-Fraumeni syndrome 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 5, 2021
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001723802.3

Allele description [Variation Report for NM_000546.6(TP53):c.946C>A (p.Pro316Thr)]

NM_000546.6(TP53):c.946C>A (p.Pro316Thr)

Gene:

TP53:tumor protein p53 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.946C>A (p.Pro316Thr)

Other names:

NM_000546.5(TP53):c.946C>A

HGVS:

NC_000017.11:g.7673582G>T
NG_017013.2:g.18969C>A
NM_000546.6:c.946C>AMANE SELECT
NM_001126112.3:c.946C>A
NM_001126113.3:c.946C>A
NM_001126114.3:c.946C>A
NM_001126115.2:c.550C>A
NM_001126116.2:c.550C>A
NM_001126117.2:c.550C>A
NM_001126118.2:c.829C>A
NM_001276695.3:c.829C>A
NM_001276696.3:c.829C>A
NM_001276697.3:c.469C>A
NM_001276698.3:c.469C>A
NM_001276699.3:c.469C>A
NM_001276760.3:c.829C>A
NM_001276761.3:c.829C>A
NP_000537.3:p.Pro316Thr
NP_000537.3:p.Pro316Thr
NP_001119584.1:p.Pro316Thr
NP_001119585.1:p.Pro316Thr
NP_001119586.1:p.Pro316Thr
NP_001119587.1:p.Pro184Thr
NP_001119588.1:p.Pro184Thr
NP_001119589.1:p.Pro184Thr
NP_001119590.1:p.Pro277Thr
NP_001263624.1:p.Pro277Thr
NP_001263625.1:p.Pro277Thr
NP_001263626.1:p.Pro157Thr
NP_001263627.1:p.Pro157Thr
NP_001263628.1:p.Pro157Thr
NP_001263689.1:p.Pro277Thr
NP_001263690.1:p.Pro277Thr
LRG_321t1:c.946C>A
LRG_321:g.18969C>A
LRG_321p1:p.Pro316Thr
NC_000017.10:g.7576900G>T
NM_000546.4:c.946C>A
NM_000546.5:c.946C>A
P04637:p.Pro316Thr

Protein change:

P157T

Links:

UniProtKB: P04637#VAR_045498; dbSNP: rs772773208

NCBI 1000 Genomes Browser:

rs772773208

Molecular consequence:

NM_000546.6:c.946C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.946C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.946C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.946C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126115.2:c.550C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126116.2:c.550C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126117.2:c.550C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.829C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276695.3:c.829C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276696.3:c.829C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276697.3:c.469C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276698.3:c.469C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276699.3:c.469C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.829C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.829C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Li-Fraumeni syndrome 1 (LFS)
Identifiers:: Gene: 553989; MedGen: C1835398; Orphanet: 524; OMIM: 151623

Recent activity

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forkhead box protein O6 [Mus musculus]
forkhead box protein O6 [Mus musculus]
gi|34610227|ref|NP_918949.1|

Protein
SRX1518388 (1)
SRA

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001949918	ClinGen TP53 Variant Curation Expert Panel, ClinGen	reviewed by expert panel (ClinGen TP53 ACMG Specifications v1.2)	Uncertain significance (Apr 5, 2021)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001949918

ClinGen TP53 Variant Curation Expert Panel, ClinGen

reviewed by expert panel

(ClinGen TP53 ACMG Specifications v1.2)

Uncertain significance
(Apr 5, 2021)

germline

curation

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation

Details of each submission

From ClinGen TP53 Variant Curation Expert Panel, ClinGen, SCV001949918.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	not provided

Description

This variant has a BayesDel score < 0.16 and Align GVGD (Zebrafish) is Class C0 (BP4). In summary, the clinical significance of TP53 c.946C>A (p.Pro316Thr) is uncertain for Li-Fraumeni syndrome. ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: BP4.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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